Multiple sequence alignment - TraesCS3B01G158300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G158300 chr3B 100.000 4227 0 0 1 4227 153606165 153610391 0.000000e+00 7806.0
1 TraesCS3B01G158300 chr3B 93.458 107 7 0 3828 3934 153649453 153649559 4.370000e-35 159.0
2 TraesCS3B01G158300 chr3B 93.220 59 3 1 3762 3820 153649453 153649510 7.530000e-13 86.1
3 TraesCS3B01G158300 chr3B 95.556 45 1 1 3931 3974 596444410 596444454 2.110000e-08 71.3
4 TraesCS3B01G158300 chr3D 93.284 3529 134 38 406 3885 102778669 102782143 0.000000e+00 5108.0
5 TraesCS3B01G158300 chr3D 87.080 387 25 7 1 380 102778309 102778677 8.460000e-112 414.0
6 TraesCS3B01G158300 chr3D 95.082 183 7 2 1753 1935 533336751 533336931 1.920000e-73 287.0
7 TraesCS3B01G158300 chr3D 91.209 91 6 2 3797 3885 102781987 102782077 5.740000e-24 122.0
8 TraesCS3B01G158300 chr3A 91.769 3341 161 47 405 3688 553000639 552997356 0.000000e+00 4542.0
9 TraesCS3B01G158300 chr3A 88.276 145 17 0 239 383 553000771 553000627 1.560000e-39 174.0
10 TraesCS3B01G158300 chr3A 77.682 233 27 13 9 227 553001033 553000812 7.420000e-23 119.0
11 TraesCS3B01G158300 chr4B 100.000 41 0 0 3934 3974 580562154 580562114 4.530000e-10 76.8
12 TraesCS3B01G158300 chr4B 95.122 41 2 0 3934 3974 625017786 625017826 9.810000e-07 65.8
13 TraesCS3B01G158300 chr5B 97.674 43 1 0 3931 3973 31288059 31288017 1.630000e-09 75.0
14 TraesCS3B01G158300 chr5D 97.619 42 1 0 3933 3974 2789764 2789723 5.860000e-09 73.1
15 TraesCS3B01G158300 chr6D 97.561 41 1 0 3933 3973 383493423 383493383 2.110000e-08 71.3
16 TraesCS3B01G158300 chr6B 100.000 38 0 0 3931 3968 591191109 591191146 2.110000e-08 71.3
17 TraesCS3B01G158300 chr6B 95.122 41 2 0 3933 3973 91854059 91854099 9.810000e-07 65.8
18 TraesCS3B01G158300 chr2B 100.000 37 0 0 3933 3969 777608762 777608726 7.580000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G158300 chr3B 153606165 153610391 4226 False 7806.000000 7806 100.000000 1 4227 1 chr3B.!!$F1 4226
1 TraesCS3B01G158300 chr3D 102778309 102782143 3834 False 1881.333333 5108 90.524333 1 3885 3 chr3D.!!$F2 3884
2 TraesCS3B01G158300 chr3A 552997356 553001033 3677 True 1611.666667 4542 85.909000 9 3688 3 chr3A.!!$R1 3679

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
200 214 0.179040 GGTCGTGGTTTGGGAAGTCA 60.179 55.000 0.00 0.0 0.0 3.41 F
311 354 1.225745 CCGCGTGAAAAGTCGATGC 60.226 57.895 4.92 0.0 0.0 3.91 F
1112 1166 1.274703 GGGAGGGATGTGGAGCAGAA 61.275 60.000 0.00 0.0 0.0 3.02 F
1293 1347 1.843206 GAGATTCCTTTGAGCCCTCCT 59.157 52.381 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1149 1.280421 AGTTTCTGCTCCACATCCCTC 59.720 52.381 0.0 0.0 0.00 4.30 R
2293 2348 0.534877 TTGAGCACTTCACGGCACAT 60.535 50.000 0.0 0.0 34.94 3.21 R
2709 2791 0.824109 CCCTCATCGTCCACTAGCAA 59.176 55.000 0.0 0.0 0.00 3.91 R
3231 3313 2.853003 GTCGAAACGATGCTAGAAGACC 59.147 50.000 0.0 0.0 38.42 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.880027 GTCAGGTTCTTGATGCCGTTT 59.120 47.619 0.00 0.00 0.00 3.60
25 26 1.879380 TCAGGTTCTTGATGCCGTTTG 59.121 47.619 0.00 0.00 0.00 2.93
67 68 1.606606 CGCTTTTGCTTTCGGATCAC 58.393 50.000 0.00 0.00 44.80 3.06
103 116 5.592104 TGTCCAGTTTTTCCCTTCTTTTC 57.408 39.130 0.00 0.00 0.00 2.29
107 120 4.408921 CCAGTTTTTCCCTTCTTTTCCCTT 59.591 41.667 0.00 0.00 0.00 3.95
108 121 5.600898 CCAGTTTTTCCCTTCTTTTCCCTTA 59.399 40.000 0.00 0.00 0.00 2.69
109 122 6.270000 CCAGTTTTTCCCTTCTTTTCCCTTAT 59.730 38.462 0.00 0.00 0.00 1.73
110 123 7.202093 CCAGTTTTTCCCTTCTTTTCCCTTATT 60.202 37.037 0.00 0.00 0.00 1.40
111 124 8.866093 CAGTTTTTCCCTTCTTTTCCCTTATTA 58.134 33.333 0.00 0.00 0.00 0.98
113 126 8.867097 GTTTTTCCCTTCTTTTCCCTTATTACT 58.133 33.333 0.00 0.00 0.00 2.24
114 127 9.442062 TTTTTCCCTTCTTTTCCCTTATTACTT 57.558 29.630 0.00 0.00 0.00 2.24
126 139 9.856162 TTTCCCTTATTACTTTTTGTCTAGTGT 57.144 29.630 0.00 0.00 0.00 3.55
199 213 1.226030 CGGTCGTGGTTTGGGAAGTC 61.226 60.000 0.00 0.00 0.00 3.01
200 214 0.179040 GGTCGTGGTTTGGGAAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
201 215 1.544759 GGTCGTGGTTTGGGAAGTCAT 60.545 52.381 0.00 0.00 0.00 3.06
202 216 2.289819 GGTCGTGGTTTGGGAAGTCATA 60.290 50.000 0.00 0.00 0.00 2.15
252 295 8.080417 ACTAATCTTAGATTGCGCGTCTTTATA 58.920 33.333 18.48 0.29 34.84 0.98
258 301 6.216750 AGATTGCGCGTCTTTATATTTCTC 57.783 37.500 8.43 0.00 0.00 2.87
268 311 6.399039 CGTCTTTATATTTCTCCGCGAGAATG 60.399 42.308 8.23 0.00 46.20 2.67
293 336 1.597663 CCCCATAATTTGACGTCTCGC 59.402 52.381 17.92 0.00 0.00 5.03
294 337 1.597663 CCCATAATTTGACGTCTCGCC 59.402 52.381 17.92 0.00 0.00 5.54
311 354 1.225745 CCGCGTGAAAAGTCGATGC 60.226 57.895 4.92 0.00 0.00 3.91
331 374 3.761218 TGCCTTCGCAGGAAAATCAAATA 59.239 39.130 4.87 0.00 44.19 1.40
372 415 4.879545 TCGGGTCATAATTTTTACTCCTGC 59.120 41.667 0.00 0.00 0.00 4.85
373 416 4.260620 CGGGTCATAATTTTTACTCCTGCG 60.261 45.833 0.00 0.00 0.00 5.18
374 417 4.036380 GGGTCATAATTTTTACTCCTGCGG 59.964 45.833 0.00 0.00 0.00 5.69
375 418 4.638865 GGTCATAATTTTTACTCCTGCGGT 59.361 41.667 0.00 0.00 0.00 5.68
376 419 5.124936 GGTCATAATTTTTACTCCTGCGGTT 59.875 40.000 0.00 0.00 0.00 4.44
377 420 6.349860 GGTCATAATTTTTACTCCTGCGGTTT 60.350 38.462 0.00 0.00 0.00 3.27
378 421 6.745907 GTCATAATTTTTACTCCTGCGGTTTC 59.254 38.462 0.00 0.00 0.00 2.78
379 422 6.657541 TCATAATTTTTACTCCTGCGGTTTCT 59.342 34.615 0.00 0.00 0.00 2.52
380 423 5.372547 AATTTTTACTCCTGCGGTTTCTC 57.627 39.130 0.00 0.00 0.00 2.87
381 424 3.764237 TTTTACTCCTGCGGTTTCTCT 57.236 42.857 0.00 0.00 0.00 3.10
382 425 4.877378 TTTTACTCCTGCGGTTTCTCTA 57.123 40.909 0.00 0.00 0.00 2.43
383 426 4.451629 TTTACTCCTGCGGTTTCTCTAG 57.548 45.455 0.00 0.00 0.00 2.43
384 427 1.926108 ACTCCTGCGGTTTCTCTAGT 58.074 50.000 0.00 0.00 0.00 2.57
385 428 2.249139 ACTCCTGCGGTTTCTCTAGTT 58.751 47.619 0.00 0.00 0.00 2.24
386 429 2.633481 ACTCCTGCGGTTTCTCTAGTTT 59.367 45.455 0.00 0.00 0.00 2.66
387 430 3.071167 ACTCCTGCGGTTTCTCTAGTTTT 59.929 43.478 0.00 0.00 0.00 2.43
388 431 4.282703 ACTCCTGCGGTTTCTCTAGTTTTA 59.717 41.667 0.00 0.00 0.00 1.52
389 432 5.046520 ACTCCTGCGGTTTCTCTAGTTTTAT 60.047 40.000 0.00 0.00 0.00 1.40
390 433 5.801380 TCCTGCGGTTTCTCTAGTTTTATT 58.199 37.500 0.00 0.00 0.00 1.40
391 434 6.235664 TCCTGCGGTTTCTCTAGTTTTATTT 58.764 36.000 0.00 0.00 0.00 1.40
392 435 6.713450 TCCTGCGGTTTCTCTAGTTTTATTTT 59.287 34.615 0.00 0.00 0.00 1.82
393 436 7.229907 TCCTGCGGTTTCTCTAGTTTTATTTTT 59.770 33.333 0.00 0.00 0.00 1.94
417 460 3.244561 TGAGGGGTTTGCAGTTTCTCTAG 60.245 47.826 0.00 0.00 0.00 2.43
474 518 2.877097 TTTCAACTGCTCCATGCCTA 57.123 45.000 0.00 0.00 42.00 3.93
482 526 1.339055 TGCTCCATGCCTATATTCCGC 60.339 52.381 0.00 0.00 42.00 5.54
483 527 1.645034 CTCCATGCCTATATTCCGCG 58.355 55.000 0.00 0.00 0.00 6.46
499 543 1.939934 CCGCGCTAATTCCATGAGAAA 59.060 47.619 5.56 0.00 38.21 2.52
549 600 4.278919 TCAACTATACATGTCCGCCGATAA 59.721 41.667 0.00 0.00 0.00 1.75
550 601 4.436242 ACTATACATGTCCGCCGATAAG 57.564 45.455 0.00 0.00 0.00 1.73
551 602 4.077108 ACTATACATGTCCGCCGATAAGA 58.923 43.478 0.00 0.00 0.00 2.10
552 603 4.705507 ACTATACATGTCCGCCGATAAGAT 59.294 41.667 0.00 0.00 0.00 2.40
553 604 5.884232 ACTATACATGTCCGCCGATAAGATA 59.116 40.000 0.00 0.00 0.00 1.98
554 605 5.654603 ATACATGTCCGCCGATAAGATAA 57.345 39.130 0.00 0.00 0.00 1.75
555 606 4.330944 ACATGTCCGCCGATAAGATAAA 57.669 40.909 0.00 0.00 0.00 1.40
556 607 4.894784 ACATGTCCGCCGATAAGATAAAT 58.105 39.130 0.00 0.00 0.00 1.40
557 608 6.032956 ACATGTCCGCCGATAAGATAAATA 57.967 37.500 0.00 0.00 0.00 1.40
558 609 6.100004 ACATGTCCGCCGATAAGATAAATAG 58.900 40.000 0.00 0.00 0.00 1.73
559 610 5.970317 TGTCCGCCGATAAGATAAATAGA 57.030 39.130 0.00 0.00 0.00 1.98
560 611 6.525578 TGTCCGCCGATAAGATAAATAGAT 57.474 37.500 0.00 0.00 0.00 1.98
561 612 6.330278 TGTCCGCCGATAAGATAAATAGATG 58.670 40.000 0.00 0.00 0.00 2.90
602 654 2.459060 TTATTCGCTGAACGGGACAA 57.541 45.000 0.00 0.00 43.89 3.18
660 712 1.383456 TTGCGCACCAAGTTCAGCTT 61.383 50.000 11.12 0.00 38.08 3.74
671 723 6.418819 CACCAAGTTCAGCTTACAATCTTTTG 59.581 38.462 0.00 0.00 35.27 2.44
759 812 4.580580 ACAAGTTTCAGGGATCTGTTTGAC 59.419 41.667 0.00 0.00 41.59 3.18
851 904 1.573108 ATGGGTCGAGGAATCACAGT 58.427 50.000 0.00 0.00 0.00 3.55
1041 1095 4.352595 TGGATTAGGAGGACCAAGTTTTCA 59.647 41.667 0.00 0.00 38.94 2.69
1056 1110 1.842720 TTTCACACACCGTCTACACG 58.157 50.000 0.00 0.00 46.29 4.49
1095 1149 1.751927 GCATGTGGCTCCTCTTGGG 60.752 63.158 0.00 0.00 40.25 4.12
1112 1166 1.274703 GGGAGGGATGTGGAGCAGAA 61.275 60.000 0.00 0.00 0.00 3.02
1185 1239 2.000429 GCAATGATGAAACAGTGGCC 58.000 50.000 0.00 0.00 36.55 5.36
1272 1326 4.005650 CCAGCAAGCAGAAGATGAGTTTA 58.994 43.478 0.00 0.00 0.00 2.01
1293 1347 1.843206 GAGATTCCTTTGAGCCCTCCT 59.157 52.381 0.00 0.00 0.00 3.69
1557 1611 4.439057 GTGTGGGATCTGATAAAAGCGTA 58.561 43.478 0.00 0.00 0.00 4.42
1670 1724 3.135348 CAGAAGGATAGCTCATGGACCAA 59.865 47.826 0.00 0.00 0.00 3.67
1900 1954 2.124736 GCCGGCCTAAGCATGACA 60.125 61.111 18.11 0.00 42.56 3.58
2076 2130 4.044426 GTGCAGAGTGTTTGGTTTGATTC 58.956 43.478 0.00 0.00 0.00 2.52
2081 2135 6.313658 GCAGAGTGTTTGGTTTGATTCTTTTT 59.686 34.615 0.00 0.00 0.00 1.94
2278 2333 7.739825 AGCTGATGTTATCTTAGGATAAGCAA 58.260 34.615 14.41 3.75 42.80 3.91
2279 2334 8.381636 AGCTGATGTTATCTTAGGATAAGCAAT 58.618 33.333 14.41 7.33 42.80 3.56
2318 2375 3.126858 TGCCGTGAAGTGCTCAAAATATC 59.873 43.478 0.00 0.00 35.22 1.63
2357 2415 7.603180 ATGTATTATGAGCTAACCAGAGTCA 57.397 36.000 0.00 0.00 0.00 3.41
2364 2422 9.982651 TTATGAGCTAACCAGAGTCAATAATAC 57.017 33.333 0.00 0.00 0.00 1.89
2365 2423 6.817184 TGAGCTAACCAGAGTCAATAATACC 58.183 40.000 0.00 0.00 0.00 2.73
2376 2434 9.334947 CAGAGTCAATAATACCAGTGAATCATT 57.665 33.333 4.25 0.00 39.35 2.57
2380 2438 9.125026 GTCAATAATACCAGTGAATCATTCCTT 57.875 33.333 0.00 0.00 0.00 3.36
2471 2553 6.549433 AGAGTTGGACCGGTTTATTACATA 57.451 37.500 9.42 0.00 0.00 2.29
2651 2733 4.142600 CCCGAGAACATCCTTTTTGATGAC 60.143 45.833 7.93 2.52 43.94 3.06
2678 2760 4.326826 TCGAGGTGAAGATTGCTGATTTT 58.673 39.130 0.00 0.00 0.00 1.82
2709 2791 4.382040 CCTGTGAGGAGACGTTATGTGATT 60.382 45.833 0.00 0.00 37.67 2.57
2852 2934 5.538067 GAAGAATTCCTTTCGAGAACCTG 57.462 43.478 0.65 0.00 39.83 4.00
2952 3034 4.365899 ACGTAATCTGAAGATGTACGCA 57.634 40.909 21.53 0.00 40.65 5.24
2973 3055 5.679601 GCATTCTCTCCTTGACTAAATCCT 58.320 41.667 0.00 0.00 0.00 3.24
3115 3197 4.584325 CAGATTGTGAAAACCCTGGAGAAA 59.416 41.667 0.00 0.00 0.00 2.52
3340 3425 8.437742 TCGATTTCGTGTTTAAAATTCTAGGAC 58.562 33.333 0.00 0.00 40.80 3.85
3410 3495 4.904895 ATCATCAGTAGCTGTATGCCAT 57.095 40.909 0.00 0.00 44.23 4.40
3450 3540 4.142071 TGTTATCTCATTCGCTCTTGCTCT 60.142 41.667 0.00 0.00 36.97 4.09
3452 3542 2.614779 TCTCATTCGCTCTTGCTCTTG 58.385 47.619 0.00 0.00 36.97 3.02
3453 3543 1.062294 CTCATTCGCTCTTGCTCTTGC 59.938 52.381 0.00 0.00 36.97 4.01
3457 3547 1.079266 CGCTCTTGCTCTTGCTCCT 60.079 57.895 0.00 0.00 40.48 3.69
3458 3548 1.360194 CGCTCTTGCTCTTGCTCCTG 61.360 60.000 0.00 0.00 40.48 3.86
3459 3549 0.321475 GCTCTTGCTCTTGCTCCTGT 60.321 55.000 0.00 0.00 40.48 4.00
3460 3550 1.724429 CTCTTGCTCTTGCTCCTGTC 58.276 55.000 0.00 0.00 40.48 3.51
3462 3552 0.676151 CTTGCTCTTGCTCCTGTCCC 60.676 60.000 0.00 0.00 40.48 4.46
3463 3553 1.130054 TTGCTCTTGCTCCTGTCCCT 61.130 55.000 0.00 0.00 40.48 4.20
3464 3554 1.078567 GCTCTTGCTCCTGTCCCTG 60.079 63.158 0.00 0.00 36.03 4.45
3465 3555 1.835927 GCTCTTGCTCCTGTCCCTGT 61.836 60.000 0.00 0.00 36.03 4.00
3466 3556 0.036577 CTCTTGCTCCTGTCCCTGTG 60.037 60.000 0.00 0.00 0.00 3.66
3467 3557 0.764369 TCTTGCTCCTGTCCCTGTGT 60.764 55.000 0.00 0.00 0.00 3.72
3472 3562 1.348036 GCTCCTGTCCCTGTGTTAAGT 59.652 52.381 0.00 0.00 0.00 2.24
3481 3571 1.455786 CCTGTGTTAAGTTCAGTCGCG 59.544 52.381 0.00 0.00 0.00 5.87
3550 3653 3.256879 TCATTATTAGCCTGCTCTCCTCG 59.743 47.826 0.00 0.00 0.00 4.63
3575 3678 6.479972 TTAGATAGAGATTGCCGAGGAAAA 57.520 37.500 0.00 0.00 0.00 2.29
3576 3679 4.954875 AGATAGAGATTGCCGAGGAAAAG 58.045 43.478 0.00 0.00 0.00 2.27
3607 3710 1.527034 CCGTCATTAGCATCATGGGG 58.473 55.000 0.00 0.00 0.00 4.96
3608 3711 1.072173 CCGTCATTAGCATCATGGGGA 59.928 52.381 0.00 0.00 0.00 4.81
3609 3712 2.487086 CCGTCATTAGCATCATGGGGAA 60.487 50.000 0.00 0.00 0.00 3.97
3610 3713 2.810274 CGTCATTAGCATCATGGGGAAG 59.190 50.000 0.00 0.00 0.00 3.46
3611 3714 3.152341 GTCATTAGCATCATGGGGAAGG 58.848 50.000 0.00 0.00 0.00 3.46
3631 3734 3.009805 AGGAAGGGCGTGGTTAATTAACT 59.990 43.478 23.89 5.42 36.47 2.24
3642 3745 7.434013 GCGTGGTTAATTAACTCAATTATTGGG 59.566 37.037 23.89 2.87 38.57 4.12
3652 3755 6.994421 ACTCAATTATTGGGTCCTTTGTTT 57.006 33.333 4.38 0.00 41.50 2.83
3671 3774 0.397564 TGTCAGCATGCCACTCTGAA 59.602 50.000 15.66 0.00 38.42 3.02
3673 3776 1.400846 GTCAGCATGCCACTCTGAATG 59.599 52.381 15.66 2.45 38.42 2.67
3695 3798 1.955778 TCATGGTGCTTTTGACCTGTG 59.044 47.619 0.00 0.00 34.26 3.66
3703 3806 0.534203 TTTTGACCTGTGAGACGGCC 60.534 55.000 0.00 0.00 0.00 6.13
3734 3837 6.280643 GTTGCTTCCCTTTTTATTCTGTTGT 58.719 36.000 0.00 0.00 0.00 3.32
3754 3858 4.137872 GATGACGCCCGGGTTCGA 62.138 66.667 24.90 11.77 39.00 3.71
3768 3872 4.436852 CCGGGTTCGAGATATGTTTGTTTG 60.437 45.833 0.00 0.00 39.00 2.93
3848 3953 5.414360 TGTTTGTTTTACTGCTGCATTTCA 58.586 33.333 1.31 0.00 0.00 2.69
3876 3981 0.533085 TTGTTGTTGCGGGATGACGA 60.533 50.000 0.00 0.00 35.47 4.20
3877 3982 1.225376 TGTTGTTGCGGGATGACGAC 61.225 55.000 0.00 0.00 35.47 4.34
3885 3990 0.389426 CGGGATGACGACTCGGTTTT 60.389 55.000 2.98 0.00 35.47 2.43
3886 3991 1.135315 CGGGATGACGACTCGGTTTTA 60.135 52.381 2.98 0.00 35.47 1.52
3887 3992 2.480759 CGGGATGACGACTCGGTTTTAT 60.481 50.000 2.98 0.00 35.47 1.40
3888 3993 3.528532 GGGATGACGACTCGGTTTTATT 58.471 45.455 2.98 0.00 0.00 1.40
3889 3994 3.937079 GGGATGACGACTCGGTTTTATTT 59.063 43.478 2.98 0.00 0.00 1.40
3890 3995 4.033702 GGGATGACGACTCGGTTTTATTTC 59.966 45.833 2.98 0.00 0.00 2.17
3891 3996 4.868734 GGATGACGACTCGGTTTTATTTCT 59.131 41.667 2.98 0.00 0.00 2.52
3892 3997 5.220416 GGATGACGACTCGGTTTTATTTCTG 60.220 44.000 2.98 0.00 0.00 3.02
3893 3998 4.624015 TGACGACTCGGTTTTATTTCTGT 58.376 39.130 2.98 0.00 0.00 3.41
3894 3999 4.446385 TGACGACTCGGTTTTATTTCTGTG 59.554 41.667 2.98 0.00 0.00 3.66
3895 4000 4.624015 ACGACTCGGTTTTATTTCTGTGA 58.376 39.130 2.98 0.00 0.00 3.58
3896 4001 5.235516 ACGACTCGGTTTTATTTCTGTGAT 58.764 37.500 2.98 0.00 0.00 3.06
3897 4002 6.392354 ACGACTCGGTTTTATTTCTGTGATA 58.608 36.000 2.98 0.00 0.00 2.15
3898 4003 7.039882 ACGACTCGGTTTTATTTCTGTGATAT 58.960 34.615 2.98 0.00 0.00 1.63
3899 4004 7.548075 ACGACTCGGTTTTATTTCTGTGATATT 59.452 33.333 2.98 0.00 0.00 1.28
3900 4005 8.388103 CGACTCGGTTTTATTTCTGTGATATTT 58.612 33.333 0.00 0.00 0.00 1.40
3902 4007 9.840427 ACTCGGTTTTATTTCTGTGATATTTTG 57.160 29.630 0.00 0.00 0.00 2.44
3903 4008 9.840427 CTCGGTTTTATTTCTGTGATATTTTGT 57.160 29.630 0.00 0.00 0.00 2.83
3910 4015 9.755804 TTATTTCTGTGATATTTTGTTGTTGCA 57.244 25.926 0.00 0.00 0.00 4.08
3911 4016 8.659925 ATTTCTGTGATATTTTGTTGTTGCAA 57.340 26.923 0.00 0.00 0.00 4.08
3912 4017 7.462109 TTCTGTGATATTTTGTTGTTGCAAC 57.538 32.000 22.83 22.83 0.00 4.17
3913 4018 6.567959 TCTGTGATATTTTGTTGTTGCAACA 58.432 32.000 27.96 27.96 37.08 3.33
3914 4019 7.208777 TCTGTGATATTTTGTTGTTGCAACAT 58.791 30.769 31.48 18.38 38.95 2.71
3915 4020 7.169476 TCTGTGATATTTTGTTGTTGCAACATG 59.831 33.333 31.48 4.35 38.95 3.21
3916 4021 6.982724 TGTGATATTTTGTTGTTGCAACATGA 59.017 30.769 31.48 18.50 38.95 3.07
3917 4022 7.042858 TGTGATATTTTGTTGTTGCAACATGAC 60.043 33.333 31.48 26.22 38.95 3.06
3918 4023 4.775440 ATTTTGTTGTTGCAACATGACG 57.225 36.364 31.48 0.00 38.95 4.35
3919 4024 2.200792 TTGTTGTTGCAACATGACGG 57.799 45.000 31.48 0.00 38.95 4.79
3920 4025 0.248825 TGTTGTTGCAACATGACGGC 60.249 50.000 31.48 17.21 38.95 5.68
3921 4026 0.030638 GTTGTTGCAACATGACGGCT 59.969 50.000 31.48 0.00 38.95 5.52
3922 4027 0.310543 TTGTTGCAACATGACGGCTC 59.689 50.000 31.48 1.04 38.95 4.70
3923 4028 1.154413 GTTGCAACATGACGGCTCG 60.154 57.895 24.52 0.00 0.00 5.03
3924 4029 2.324330 TTGCAACATGACGGCTCGG 61.324 57.895 0.00 0.00 0.00 4.63
3925 4030 2.742372 GCAACATGACGGCTCGGT 60.742 61.111 0.00 0.00 0.00 4.69
3926 4031 2.325082 GCAACATGACGGCTCGGTT 61.325 57.895 0.00 0.00 0.00 4.44
3927 4032 1.852067 GCAACATGACGGCTCGGTTT 61.852 55.000 0.00 0.00 0.00 3.27
3928 4033 0.110238 CAACATGACGGCTCGGTTTG 60.110 55.000 0.00 0.00 0.00 2.93
3929 4034 1.234615 AACATGACGGCTCGGTTTGG 61.235 55.000 0.00 0.00 0.00 3.28
3930 4035 1.375396 CATGACGGCTCGGTTTGGA 60.375 57.895 0.00 0.00 0.00 3.53
3931 4036 0.744414 CATGACGGCTCGGTTTGGAT 60.744 55.000 0.00 0.00 0.00 3.41
3932 4037 0.828022 ATGACGGCTCGGTTTGGATA 59.172 50.000 0.00 0.00 0.00 2.59
3933 4038 0.828022 TGACGGCTCGGTTTGGATAT 59.172 50.000 0.00 0.00 0.00 1.63
3934 4039 2.033372 TGACGGCTCGGTTTGGATATA 58.967 47.619 0.00 0.00 0.00 0.86
3935 4040 2.223876 TGACGGCTCGGTTTGGATATAC 60.224 50.000 0.00 0.00 0.00 1.47
3936 4041 2.035576 GACGGCTCGGTTTGGATATACT 59.964 50.000 0.00 0.00 0.00 2.12
3937 4042 2.035576 ACGGCTCGGTTTGGATATACTC 59.964 50.000 0.00 0.00 0.00 2.59
3938 4043 2.609737 CGGCTCGGTTTGGATATACTCC 60.610 54.545 0.00 0.00 45.19 3.85
3939 4044 2.289506 GGCTCGGTTTGGATATACTCCC 60.290 54.545 0.00 0.00 44.23 4.30
3940 4045 2.633481 GCTCGGTTTGGATATACTCCCT 59.367 50.000 0.00 0.00 44.23 4.20
3941 4046 3.306156 GCTCGGTTTGGATATACTCCCTC 60.306 52.174 0.00 0.00 44.23 4.30
3942 4047 3.236896 TCGGTTTGGATATACTCCCTCC 58.763 50.000 0.00 0.00 44.23 4.30
3943 4048 2.029290 CGGTTTGGATATACTCCCTCCG 60.029 54.545 0.00 0.00 44.23 4.63
3944 4049 2.970640 GGTTTGGATATACTCCCTCCGT 59.029 50.000 0.00 0.00 44.23 4.69
3945 4050 3.006644 GGTTTGGATATACTCCCTCCGTC 59.993 52.174 0.00 0.00 44.23 4.79
3946 4051 2.599408 TGGATATACTCCCTCCGTCC 57.401 55.000 0.00 0.00 44.23 4.79
3947 4052 2.071372 TGGATATACTCCCTCCGTCCT 58.929 52.381 0.00 0.00 44.23 3.85
3948 4053 3.262842 TGGATATACTCCCTCCGTCCTA 58.737 50.000 0.00 0.00 44.23 2.94
3949 4054 3.659195 TGGATATACTCCCTCCGTCCTAA 59.341 47.826 0.00 0.00 44.23 2.69
3950 4055 4.106825 TGGATATACTCCCTCCGTCCTAAA 59.893 45.833 0.00 0.00 44.23 1.85
3951 4056 5.082425 GGATATACTCCCTCCGTCCTAAAA 58.918 45.833 0.00 0.00 38.19 1.52
3952 4057 5.720520 GGATATACTCCCTCCGTCCTAAAAT 59.279 44.000 0.00 0.00 38.19 1.82
3953 4058 6.212993 GGATATACTCCCTCCGTCCTAAAATT 59.787 42.308 0.00 0.00 38.19 1.82
3954 4059 5.970501 ATACTCCCTCCGTCCTAAAATTT 57.029 39.130 0.00 0.00 0.00 1.82
3955 4060 4.652679 ACTCCCTCCGTCCTAAAATTTT 57.347 40.909 8.75 8.75 0.00 1.82
3956 4061 4.994282 ACTCCCTCCGTCCTAAAATTTTT 58.006 39.130 9.06 0.00 0.00 1.94
3957 4062 4.765339 ACTCCCTCCGTCCTAAAATTTTTG 59.235 41.667 9.06 7.07 0.00 2.44
3958 4063 4.732065 TCCCTCCGTCCTAAAATTTTTGT 58.268 39.130 9.06 0.00 0.00 2.83
3959 4064 4.763279 TCCCTCCGTCCTAAAATTTTTGTC 59.237 41.667 9.06 2.40 0.00 3.18
3960 4065 4.765339 CCCTCCGTCCTAAAATTTTTGTCT 59.235 41.667 9.06 0.00 0.00 3.41
3961 4066 5.243060 CCCTCCGTCCTAAAATTTTTGTCTT 59.757 40.000 9.06 0.00 0.00 3.01
3962 4067 6.431852 CCCTCCGTCCTAAAATTTTTGTCTTA 59.568 38.462 9.06 0.00 0.00 2.10
3963 4068 7.361799 CCCTCCGTCCTAAAATTTTTGTCTTAG 60.362 40.741 9.06 0.00 0.00 2.18
3964 4069 7.389607 CCTCCGTCCTAAAATTTTTGTCTTAGA 59.610 37.037 9.06 0.00 0.00 2.10
3965 4070 8.857694 TCCGTCCTAAAATTTTTGTCTTAGAT 57.142 30.769 9.06 0.00 0.00 1.98
3966 4071 9.292195 TCCGTCCTAAAATTTTTGTCTTAGATT 57.708 29.630 9.06 0.00 0.00 2.40
3967 4072 9.908152 CCGTCCTAAAATTTTTGTCTTAGATTT 57.092 29.630 9.06 0.00 0.00 2.17
3970 4075 9.705290 TCCTAAAATTTTTGTCTTAGATTTGCC 57.295 29.630 9.06 0.00 0.00 4.52
3971 4076 9.710900 CCTAAAATTTTTGTCTTAGATTTGCCT 57.289 29.630 9.06 0.00 0.00 4.75
3974 4079 9.710900 AAAATTTTTGTCTTAGATTTGCCTAGG 57.289 29.630 3.67 3.67 0.00 3.02
3975 4080 5.897377 TTTTGTCTTAGATTTGCCTAGGC 57.103 39.130 27.71 27.71 42.35 3.93
3987 4092 0.521735 GCCTAGGCAAACTGAAACGG 59.478 55.000 29.33 0.00 41.49 4.44
3988 4093 1.165270 CCTAGGCAAACTGAAACGGG 58.835 55.000 0.00 0.00 0.00 5.28
3989 4094 0.521735 CTAGGCAAACTGAAACGGGC 59.478 55.000 0.00 0.00 0.00 6.13
3990 4095 1.231958 TAGGCAAACTGAAACGGGCG 61.232 55.000 0.00 0.00 0.00 6.13
3991 4096 2.050442 GCAAACTGAAACGGGCGG 60.050 61.111 0.00 0.00 0.00 6.13
3992 4097 2.548295 GCAAACTGAAACGGGCGGA 61.548 57.895 0.00 0.00 0.00 5.54
3993 4098 1.281656 CAAACTGAAACGGGCGGAC 59.718 57.895 0.00 0.00 0.00 4.79
3994 4099 2.248835 AAACTGAAACGGGCGGACG 61.249 57.895 0.00 0.00 40.31 4.79
3995 4100 2.647680 AAACTGAAACGGGCGGACGA 62.648 55.000 0.00 0.00 37.61 4.20
3996 4101 2.125673 CTGAAACGGGCGGACGAT 60.126 61.111 0.00 0.00 37.61 3.73
3997 4102 2.433491 TGAAACGGGCGGACGATG 60.433 61.111 0.00 0.00 37.61 3.84
3998 4103 3.192922 GAAACGGGCGGACGATGG 61.193 66.667 0.00 0.00 37.61 3.51
3999 4104 4.770874 AAACGGGCGGACGATGGG 62.771 66.667 0.00 0.00 37.61 4.00
4015 4120 2.638480 TGGGACAGGACACAAAGAAG 57.362 50.000 0.00 0.00 0.00 2.85
4016 4121 2.123589 TGGGACAGGACACAAAGAAGA 58.876 47.619 0.00 0.00 0.00 2.87
4017 4122 2.711009 TGGGACAGGACACAAAGAAGAT 59.289 45.455 0.00 0.00 0.00 2.40
4018 4123 3.077359 GGGACAGGACACAAAGAAGATG 58.923 50.000 0.00 0.00 0.00 2.90
4019 4124 3.077359 GGACAGGACACAAAGAAGATGG 58.923 50.000 0.00 0.00 0.00 3.51
4020 4125 2.485814 GACAGGACACAAAGAAGATGGC 59.514 50.000 0.00 0.00 0.00 4.40
4021 4126 2.107204 ACAGGACACAAAGAAGATGGCT 59.893 45.455 0.00 0.00 0.00 4.75
4022 4127 2.486982 CAGGACACAAAGAAGATGGCTG 59.513 50.000 0.00 0.00 0.00 4.85
4023 4128 1.200948 GGACACAAAGAAGATGGCTGC 59.799 52.381 0.00 0.00 0.00 5.25
4024 4129 1.200948 GACACAAAGAAGATGGCTGCC 59.799 52.381 12.87 12.87 0.00 4.85
4025 4130 0.529378 CACAAAGAAGATGGCTGCCC 59.471 55.000 17.53 0.80 0.00 5.36
4026 4131 0.613012 ACAAAGAAGATGGCTGCCCC 60.613 55.000 17.53 8.18 0.00 5.80
4027 4132 1.000866 AAAGAAGATGGCTGCCCCC 59.999 57.895 17.53 7.79 0.00 5.40
4028 4133 1.513087 AAAGAAGATGGCTGCCCCCT 61.513 55.000 17.53 10.17 0.00 4.79
4029 4134 2.123982 GAAGATGGCTGCCCCCTG 60.124 66.667 17.53 0.00 0.00 4.45
4030 4135 4.453892 AAGATGGCTGCCCCCTGC 62.454 66.667 17.53 0.68 41.77 4.85
4032 4137 4.891037 GATGGCTGCCCCCTGCTC 62.891 72.222 17.53 0.00 42.00 4.26
4040 4145 4.247380 CCCCCTGCTCTGGCGATC 62.247 72.222 0.00 0.00 42.25 3.69
4041 4146 4.247380 CCCCTGCTCTGGCGATCC 62.247 72.222 0.00 0.00 42.25 3.36
4042 4147 4.247380 CCCTGCTCTGGCGATCCC 62.247 72.222 0.00 0.00 42.25 3.85
4043 4148 4.598894 CCTGCTCTGGCGATCCCG 62.599 72.222 0.00 0.00 42.25 5.14
4044 4149 3.842923 CTGCTCTGGCGATCCCGT 61.843 66.667 0.00 0.00 42.25 5.28
4045 4150 3.781770 CTGCTCTGGCGATCCCGTC 62.782 68.421 0.00 0.00 42.25 4.79
4094 4199 4.796495 CCCTTTCCGCCCCCTTCG 62.796 72.222 0.00 0.00 0.00 3.79
4119 4224 4.143333 CCTCGTTCCGGCGGATGT 62.143 66.667 31.59 0.00 0.00 3.06
4120 4225 2.885644 CTCGTTCCGGCGGATGTG 60.886 66.667 31.59 21.51 0.00 3.21
4121 4226 3.642778 CTCGTTCCGGCGGATGTGT 62.643 63.158 31.59 0.00 0.00 3.72
4122 4227 3.186047 CGTTCCGGCGGATGTGTC 61.186 66.667 31.59 15.96 0.00 3.67
4123 4228 3.186047 GTTCCGGCGGATGTGTCG 61.186 66.667 31.59 0.00 0.00 4.35
4130 4235 4.873129 CGGATGTGTCGCCCCTCG 62.873 72.222 0.00 0.00 40.15 4.63
4153 4258 4.587189 CCGGACGCCCCTTCGATC 62.587 72.222 0.00 0.00 0.00 3.69
4154 4259 4.925576 CGGACGCCCCTTCGATCG 62.926 72.222 9.36 9.36 0.00 3.69
4200 4305 2.125106 GGACTGTGCCGATGACCC 60.125 66.667 0.00 0.00 0.00 4.46
4201 4306 2.125106 GACTGTGCCGATGACCCC 60.125 66.667 0.00 0.00 0.00 4.95
4202 4307 3.682292 GACTGTGCCGATGACCCCC 62.682 68.421 0.00 0.00 0.00 5.40
4216 4321 3.744155 CCCCCTTTCCTGCTCCCC 61.744 72.222 0.00 0.00 0.00 4.81
4217 4322 4.115199 CCCCTTTCCTGCTCCCCG 62.115 72.222 0.00 0.00 0.00 5.73
4218 4323 4.803908 CCCTTTCCTGCTCCCCGC 62.804 72.222 0.00 0.00 39.77 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.644418 GCACAGATTTGCACGCCA 59.356 55.556 0.00 0.00 42.49 5.69
25 26 2.502510 CGCACAGATTTGCACGCC 60.503 61.111 0.00 0.00 43.15 5.68
51 52 1.269448 GGCAGTGATCCGAAAGCAAAA 59.731 47.619 0.00 0.00 0.00 2.44
67 68 3.792716 GGACAAATCCAAACGGCAG 57.207 52.632 0.00 0.00 45.47 4.85
103 116 8.842358 TGACACTAGACAAAAAGTAATAAGGG 57.158 34.615 0.00 0.00 0.00 3.95
109 122 9.444600 ACTTTTCTGACACTAGACAAAAAGTAA 57.555 29.630 20.98 5.85 37.98 2.24
110 123 9.444600 AACTTTTCTGACACTAGACAAAAAGTA 57.555 29.630 21.62 2.79 38.29 2.24
111 124 7.923414 ACTTTTCTGACACTAGACAAAAAGT 57.077 32.000 19.31 19.31 36.80 2.66
113 126 8.330466 TGAACTTTTCTGACACTAGACAAAAA 57.670 30.769 0.00 3.96 0.00 1.94
114 127 7.065803 CCTGAACTTTTCTGACACTAGACAAAA 59.934 37.037 0.00 0.00 0.00 2.44
121 134 6.097839 ACACTACCTGAACTTTTCTGACACTA 59.902 38.462 0.00 0.00 0.00 2.74
126 139 4.574828 GCAACACTACCTGAACTTTTCTGA 59.425 41.667 0.00 0.00 0.00 3.27
199 213 2.411748 CACGCCGCCAGTATTATGTATG 59.588 50.000 0.00 0.00 0.00 2.39
200 214 2.036733 ACACGCCGCCAGTATTATGTAT 59.963 45.455 0.00 0.00 0.00 2.29
201 215 1.409790 ACACGCCGCCAGTATTATGTA 59.590 47.619 0.00 0.00 0.00 2.29
202 216 0.177141 ACACGCCGCCAGTATTATGT 59.823 50.000 0.00 0.00 0.00 2.29
293 336 1.225745 GCATCGACTTTTCACGCGG 60.226 57.895 12.47 0.00 0.00 6.46
294 337 1.225745 GGCATCGACTTTTCACGCG 60.226 57.895 3.53 3.53 0.00 6.01
311 354 5.355350 AGACTATTTGATTTTCCTGCGAAGG 59.645 40.000 1.59 1.59 0.00 3.46
316 359 6.319658 TCATCCAGACTATTTGATTTTCCTGC 59.680 38.462 0.00 0.00 0.00 4.85
331 374 2.625737 CGAACAAGCATCATCCAGACT 58.374 47.619 0.00 0.00 0.00 3.24
391 434 3.517500 AGAAACTGCAAACCCCTCAAAAA 59.482 39.130 0.00 0.00 0.00 1.94
392 435 3.103742 AGAAACTGCAAACCCCTCAAAA 58.896 40.909 0.00 0.00 0.00 2.44
393 436 2.693074 GAGAAACTGCAAACCCCTCAAA 59.307 45.455 0.00 0.00 0.00 2.69
394 437 2.091885 AGAGAAACTGCAAACCCCTCAA 60.092 45.455 0.00 0.00 0.00 3.02
395 438 1.494721 AGAGAAACTGCAAACCCCTCA 59.505 47.619 0.00 0.00 0.00 3.86
396 439 2.278332 AGAGAAACTGCAAACCCCTC 57.722 50.000 0.00 0.00 0.00 4.30
397 440 2.711547 ACTAGAGAAACTGCAAACCCCT 59.288 45.455 0.00 0.00 0.00 4.79
398 441 2.814336 CACTAGAGAAACTGCAAACCCC 59.186 50.000 0.00 0.00 0.00 4.95
399 442 3.740115 TCACTAGAGAAACTGCAAACCC 58.260 45.455 0.00 0.00 0.00 4.11
400 443 5.470098 TGAATCACTAGAGAAACTGCAAACC 59.530 40.000 0.00 0.00 0.00 3.27
401 444 6.017934 TGTGAATCACTAGAGAAACTGCAAAC 60.018 38.462 14.97 0.00 35.11 2.93
402 445 6.054941 TGTGAATCACTAGAGAAACTGCAAA 58.945 36.000 14.97 0.00 35.11 3.68
403 446 5.610398 TGTGAATCACTAGAGAAACTGCAA 58.390 37.500 14.97 0.00 35.11 4.08
404 447 5.213891 TGTGAATCACTAGAGAAACTGCA 57.786 39.130 14.97 0.00 35.11 4.41
405 448 5.233988 ACTGTGAATCACTAGAGAAACTGC 58.766 41.667 14.97 0.00 35.11 4.40
417 460 5.186996 ACAATTGGACAACTGTGAATCAC 57.813 39.130 10.83 6.41 28.82 3.06
474 518 3.935203 CTCATGGAATTAGCGCGGAATAT 59.065 43.478 8.83 0.00 0.00 1.28
482 526 6.182039 TGACTTTTTCTCATGGAATTAGCG 57.818 37.500 0.00 0.00 33.53 4.26
483 527 8.992835 ATTTGACTTTTTCTCATGGAATTAGC 57.007 30.769 0.00 0.00 33.53 3.09
519 563 7.307751 CGGCGGACATGTATAGTTGAATTTAAT 60.308 37.037 0.00 0.00 0.00 1.40
521 565 5.464057 CGGCGGACATGTATAGTTGAATTTA 59.536 40.000 0.00 0.00 0.00 1.40
522 566 4.272504 CGGCGGACATGTATAGTTGAATTT 59.727 41.667 0.00 0.00 0.00 1.82
534 585 4.330944 TTTATCTTATCGGCGGACATGT 57.669 40.909 7.21 0.00 0.00 3.21
535 586 6.330278 TCTATTTATCTTATCGGCGGACATG 58.670 40.000 7.21 0.00 0.00 3.21
539 590 6.769134 TCATCTATTTATCTTATCGGCGGA 57.231 37.500 7.21 0.00 0.00 5.54
759 812 1.417890 AGGTCAAGGGTCTGTTCAGTG 59.582 52.381 0.00 0.00 0.00 3.66
851 904 2.119495 GAGACCTTAGGCCAGGAATCA 58.881 52.381 15.94 0.00 37.39 2.57
1021 1075 5.070685 GTGTGAAAACTTGGTCCTCCTAAT 58.929 41.667 0.00 0.00 34.23 1.73
1032 1086 3.619483 TGTAGACGGTGTGTGAAAACTTG 59.381 43.478 0.00 0.00 0.00 3.16
1041 1095 1.521450 CCCTCGTGTAGACGGTGTGT 61.521 60.000 12.92 0.00 46.11 3.72
1095 1149 1.280421 AGTTTCTGCTCCACATCCCTC 59.720 52.381 0.00 0.00 0.00 4.30
1112 1166 3.281727 TGCTCACAAACCTCTGAAGTT 57.718 42.857 0.00 0.00 0.00 2.66
1272 1326 1.843206 GGAGGGCTCAAAGGAATCTCT 59.157 52.381 0.00 0.00 0.00 3.10
1293 1347 3.822735 CCTTGGATTTCTCAGACTTTGCA 59.177 43.478 0.00 0.00 0.00 4.08
1422 1476 2.591571 TCAGCTTGTGATGAGATCCG 57.408 50.000 0.00 0.00 33.24 4.18
1670 1724 5.269554 TCCCCCATTGTCAAAGTATCTTT 57.730 39.130 0.00 0.00 0.00 2.52
1900 1954 2.126882 TGCAGCTATTATCCCACCAGT 58.873 47.619 0.00 0.00 0.00 4.00
2076 2130 8.519799 TGACCATTATAAGGCTAAGGAAAAAG 57.480 34.615 0.00 0.00 0.00 2.27
2081 2135 5.073008 TGCATGACCATTATAAGGCTAAGGA 59.927 40.000 0.00 0.00 0.00 3.36
2245 2300 9.988815 TCCTAAGATAACATCAGCTTAATCTTC 57.011 33.333 0.00 0.00 0.00 2.87
2255 2310 9.499479 ACATTGCTTATCCTAAGATAACATCAG 57.501 33.333 0.00 0.00 39.53 2.90
2278 2333 4.175516 CGGCACATTGAAAATAGCAACAT 58.824 39.130 0.00 0.00 0.00 2.71
2279 2334 3.005261 ACGGCACATTGAAAATAGCAACA 59.995 39.130 0.00 0.00 0.00 3.33
2293 2348 0.534877 TTGAGCACTTCACGGCACAT 60.535 50.000 0.00 0.00 34.94 3.21
2332 2389 8.706322 TGACTCTGGTTAGCTCATAATACATA 57.294 34.615 0.00 0.00 0.00 2.29
2333 2390 7.603180 TGACTCTGGTTAGCTCATAATACAT 57.397 36.000 0.00 0.00 0.00 2.29
2335 2392 9.982651 TTATTGACTCTGGTTAGCTCATAATAC 57.017 33.333 0.00 0.00 0.00 1.89
2347 2405 6.620877 TCACTGGTATTATTGACTCTGGTT 57.379 37.500 0.00 0.00 0.00 3.67
2357 2415 9.479549 AACAAGGAATGATTCACTGGTATTATT 57.520 29.630 7.56 0.00 0.00 1.40
2364 2422 7.395190 TCAATAACAAGGAATGATTCACTGG 57.605 36.000 7.56 2.49 0.00 4.00
2376 2434 8.160765 TCAGACAAGGTTAATCAATAACAAGGA 58.839 33.333 1.32 0.00 44.77 3.36
2471 2553 2.838202 TCCAGGAAGAAGCTCCGTAATT 59.162 45.455 0.00 0.00 40.75 1.40
2651 2733 3.070018 AGCAATCTTCACCTCGAACTTG 58.930 45.455 0.00 0.00 0.00 3.16
2709 2791 0.824109 CCCTCATCGTCCACTAGCAA 59.176 55.000 0.00 0.00 0.00 3.91
2852 2934 4.035102 GCCACCTGGACTGGGGAC 62.035 72.222 0.00 0.00 37.39 4.46
2952 3034 7.613411 CCAAAAGGATTTAGTCAAGGAGAGAAT 59.387 37.037 0.00 0.00 37.28 2.40
3115 3197 3.525537 CTGCGACATAACAGACTGGATT 58.474 45.455 7.51 0.00 35.90 3.01
3231 3313 2.853003 GTCGAAACGATGCTAGAAGACC 59.147 50.000 0.00 0.00 38.42 3.85
3340 3425 3.186409 CACCTAATAAACATCCGCATCCG 59.814 47.826 0.00 0.00 0.00 4.18
3383 3468 6.652481 GGCATACAGCTACTGATGATAAATGT 59.348 38.462 0.78 0.00 44.79 2.71
3384 3469 6.652062 TGGCATACAGCTACTGATGATAAATG 59.348 38.462 0.78 0.00 44.79 2.32
3386 3471 6.173427 TGGCATACAGCTACTGATGATAAA 57.827 37.500 0.78 0.00 44.79 1.40
3387 3472 5.806654 TGGCATACAGCTACTGATGATAA 57.193 39.130 0.78 0.00 44.79 1.75
3388 3473 7.666063 ATATGGCATACAGCTACTGATGATA 57.334 36.000 9.83 0.00 44.79 2.15
3394 3479 7.821359 AGTTTGATATATGGCATACAGCTACTG 59.179 37.037 9.83 0.00 44.79 2.74
3450 3540 1.429930 TAACACAGGGACAGGAGCAA 58.570 50.000 0.00 0.00 0.00 3.91
3452 3542 1.348036 ACTTAACACAGGGACAGGAGC 59.652 52.381 0.00 0.00 0.00 4.70
3453 3543 3.071023 TGAACTTAACACAGGGACAGGAG 59.929 47.826 0.00 0.00 0.00 3.69
3457 3547 3.491964 CGACTGAACTTAACACAGGGACA 60.492 47.826 0.00 0.00 36.17 4.02
3458 3548 3.057734 CGACTGAACTTAACACAGGGAC 58.942 50.000 0.00 0.00 36.17 4.46
3459 3549 2.547218 GCGACTGAACTTAACACAGGGA 60.547 50.000 0.00 0.00 36.17 4.20
3460 3550 1.798813 GCGACTGAACTTAACACAGGG 59.201 52.381 0.00 0.00 36.17 4.45
3462 3552 1.455786 CCGCGACTGAACTTAACACAG 59.544 52.381 8.23 0.00 37.62 3.66
3463 3553 1.202440 ACCGCGACTGAACTTAACACA 60.202 47.619 8.23 0.00 0.00 3.72
3464 3554 1.191647 CACCGCGACTGAACTTAACAC 59.808 52.381 8.23 0.00 0.00 3.32
3465 3555 1.493772 CACCGCGACTGAACTTAACA 58.506 50.000 8.23 0.00 0.00 2.41
3466 3556 0.163146 GCACCGCGACTGAACTTAAC 59.837 55.000 8.23 0.00 0.00 2.01
3467 3557 0.249531 TGCACCGCGACTGAACTTAA 60.250 50.000 8.23 0.00 0.00 1.85
3472 3562 0.245266 TAATCTGCACCGCGACTGAA 59.755 50.000 8.23 0.00 0.00 3.02
3481 3571 5.700832 TCGACCAATATGAATAATCTGCACC 59.299 40.000 0.00 0.00 0.00 5.01
3518 3608 8.601047 AGCAGGCTAATAATGATGACTATCTA 57.399 34.615 0.00 0.00 34.31 1.98
3521 3611 7.364585 GGAGAGCAGGCTAATAATGATGACTAT 60.365 40.741 0.00 0.00 0.00 2.12
3529 3619 3.006323 ACGAGGAGAGCAGGCTAATAATG 59.994 47.826 0.00 0.00 0.00 1.90
3550 3653 5.455056 TCCTCGGCAATCTCTATCTAAAC 57.545 43.478 0.00 0.00 0.00 2.01
3591 3694 3.055328 TCCTTCCCCATGATGCTAATGA 58.945 45.455 0.00 0.00 0.00 2.57
3607 3710 2.124277 ATTAACCACGCCCTTCCTTC 57.876 50.000 0.00 0.00 0.00 3.46
3608 3711 2.597578 AATTAACCACGCCCTTCCTT 57.402 45.000 0.00 0.00 0.00 3.36
3609 3712 3.009805 AGTTAATTAACCACGCCCTTCCT 59.990 43.478 21.92 0.00 36.88 3.36
3610 3713 3.349927 AGTTAATTAACCACGCCCTTCC 58.650 45.455 21.92 0.00 36.88 3.46
3611 3714 4.004982 TGAGTTAATTAACCACGCCCTTC 58.995 43.478 21.92 12.23 36.88 3.46
3631 3734 6.325028 TGACAAACAAAGGACCCAATAATTGA 59.675 34.615 0.00 0.00 0.00 2.57
3642 3745 2.397549 GCATGCTGACAAACAAAGGAC 58.602 47.619 11.37 0.00 0.00 3.85
3643 3746 1.340889 GGCATGCTGACAAACAAAGGA 59.659 47.619 18.92 0.00 0.00 3.36
3652 3755 0.397564 TTCAGAGTGGCATGCTGACA 59.602 50.000 18.92 4.09 38.30 3.58
3703 3806 2.994643 AAAGGGAAGCAACCGGGGTG 62.995 60.000 7.98 7.98 0.00 4.61
3714 3817 5.538433 TCCCACAACAGAATAAAAAGGGAAG 59.462 40.000 0.00 0.00 39.69 3.46
3715 3818 5.459505 TCCCACAACAGAATAAAAAGGGAA 58.540 37.500 0.00 0.00 39.69 3.97
3716 3819 5.068215 TCCCACAACAGAATAAAAAGGGA 57.932 39.130 0.00 0.00 40.31 4.20
3717 3820 5.480073 TCATCCCACAACAGAATAAAAAGGG 59.520 40.000 0.00 0.00 35.09 3.95
3718 3821 6.389906 GTCATCCCACAACAGAATAAAAAGG 58.610 40.000 0.00 0.00 0.00 3.11
3749 3853 6.736853 GCAGTACAAACAAACATATCTCGAAC 59.263 38.462 0.00 0.00 0.00 3.95
3754 3858 5.473162 TGCAGCAGTACAAACAAACATATCT 59.527 36.000 0.00 0.00 0.00 1.98
3848 3953 2.415357 CCCGCAACAACAAAATATCGCT 60.415 45.455 0.00 0.00 0.00 4.93
3850 3955 3.479505 TCCCGCAACAACAAAATATCG 57.520 42.857 0.00 0.00 0.00 2.92
3876 3981 9.840427 CAAAATATCACAGAAATAAAACCGAGT 57.160 29.630 0.00 0.00 0.00 4.18
3877 3982 9.840427 ACAAAATATCACAGAAATAAAACCGAG 57.160 29.630 0.00 0.00 0.00 4.63
3885 3990 9.755804 TTGCAACAACAAAATATCACAGAAATA 57.244 25.926 0.00 0.00 0.00 1.40
3886 3991 8.550376 GTTGCAACAACAAAATATCACAGAAAT 58.450 29.630 24.52 0.00 0.00 2.17
3887 3992 7.547019 TGTTGCAACAACAAAATATCACAGAAA 59.453 29.630 29.36 0.00 35.67 2.52
3888 3993 7.038048 TGTTGCAACAACAAAATATCACAGAA 58.962 30.769 29.36 0.00 35.67 3.02
3889 3994 6.567959 TGTTGCAACAACAAAATATCACAGA 58.432 32.000 29.36 0.00 35.67 3.41
3890 3995 6.825284 TGTTGCAACAACAAAATATCACAG 57.175 33.333 29.36 0.00 35.67 3.66
3891 3996 6.982724 TCATGTTGCAACAACAAAATATCACA 59.017 30.769 34.06 8.48 43.03 3.58
3892 3997 7.282916 GTCATGTTGCAACAACAAAATATCAC 58.717 34.615 34.06 9.97 43.03 3.06
3893 3998 6.143598 CGTCATGTTGCAACAACAAAATATCA 59.856 34.615 34.06 8.37 43.03 2.15
3894 3999 6.399880 CCGTCATGTTGCAACAACAAAATATC 60.400 38.462 34.06 15.68 43.03 1.63
3895 4000 5.404968 CCGTCATGTTGCAACAACAAAATAT 59.595 36.000 34.06 13.97 43.03 1.28
3896 4001 4.742167 CCGTCATGTTGCAACAACAAAATA 59.258 37.500 34.06 10.37 43.03 1.40
3897 4002 3.555139 CCGTCATGTTGCAACAACAAAAT 59.445 39.130 34.06 15.48 43.03 1.82
3898 4003 2.926200 CCGTCATGTTGCAACAACAAAA 59.074 40.909 34.06 15.77 43.03 2.44
3899 4004 2.534298 CCGTCATGTTGCAACAACAAA 58.466 42.857 34.06 17.45 43.03 2.83
3900 4005 1.800655 GCCGTCATGTTGCAACAACAA 60.801 47.619 34.06 19.82 43.03 2.83
3901 4006 0.248825 GCCGTCATGTTGCAACAACA 60.249 50.000 34.06 21.06 43.03 3.33
3902 4007 0.030638 AGCCGTCATGTTGCAACAAC 59.969 50.000 34.06 26.25 43.03 3.32
3903 4008 0.310543 GAGCCGTCATGTTGCAACAA 59.689 50.000 34.06 17.77 43.03 2.83
3904 4009 1.840630 CGAGCCGTCATGTTGCAACA 61.841 55.000 32.78 32.78 44.06 3.33
3905 4010 1.154413 CGAGCCGTCATGTTGCAAC 60.154 57.895 22.83 22.83 0.00 4.17
3906 4011 2.324330 CCGAGCCGTCATGTTGCAA 61.324 57.895 0.00 0.00 0.00 4.08
3907 4012 2.741985 CCGAGCCGTCATGTTGCA 60.742 61.111 0.00 0.00 0.00 4.08
3908 4013 1.852067 AAACCGAGCCGTCATGTTGC 61.852 55.000 0.00 0.00 0.00 4.17
3909 4014 0.110238 CAAACCGAGCCGTCATGTTG 60.110 55.000 0.00 0.00 0.00 3.33
3910 4015 1.234615 CCAAACCGAGCCGTCATGTT 61.235 55.000 0.00 0.00 0.00 2.71
3911 4016 1.671054 CCAAACCGAGCCGTCATGT 60.671 57.895 0.00 0.00 0.00 3.21
3912 4017 0.744414 ATCCAAACCGAGCCGTCATG 60.744 55.000 0.00 0.00 0.00 3.07
3913 4018 0.828022 TATCCAAACCGAGCCGTCAT 59.172 50.000 0.00 0.00 0.00 3.06
3914 4019 0.828022 ATATCCAAACCGAGCCGTCA 59.172 50.000 0.00 0.00 0.00 4.35
3915 4020 2.035576 AGTATATCCAAACCGAGCCGTC 59.964 50.000 0.00 0.00 0.00 4.79
3916 4021 2.035576 GAGTATATCCAAACCGAGCCGT 59.964 50.000 0.00 0.00 0.00 5.68
3917 4022 2.673833 GAGTATATCCAAACCGAGCCG 58.326 52.381 0.00 0.00 0.00 5.52
3929 4034 6.854091 ATTTTAGGACGGAGGGAGTATATC 57.146 41.667 0.00 0.00 0.00 1.63
3930 4035 7.628501 AAATTTTAGGACGGAGGGAGTATAT 57.371 36.000 0.00 0.00 0.00 0.86
3931 4036 7.441903 AAAATTTTAGGACGGAGGGAGTATA 57.558 36.000 0.37 0.00 0.00 1.47
3932 4037 5.970501 AAATTTTAGGACGGAGGGAGTAT 57.029 39.130 0.00 0.00 0.00 2.12
3933 4038 5.767277 AAAATTTTAGGACGGAGGGAGTA 57.233 39.130 0.37 0.00 0.00 2.59
3934 4039 4.652679 AAAATTTTAGGACGGAGGGAGT 57.347 40.909 0.37 0.00 0.00 3.85
3935 4040 4.765339 ACAAAAATTTTAGGACGGAGGGAG 59.235 41.667 3.34 0.00 0.00 4.30
3936 4041 4.732065 ACAAAAATTTTAGGACGGAGGGA 58.268 39.130 3.34 0.00 0.00 4.20
3937 4042 4.765339 AGACAAAAATTTTAGGACGGAGGG 59.235 41.667 3.34 0.00 0.00 4.30
3938 4043 5.959618 AGACAAAAATTTTAGGACGGAGG 57.040 39.130 3.34 0.00 0.00 4.30
3939 4044 8.319143 TCTAAGACAAAAATTTTAGGACGGAG 57.681 34.615 3.34 4.15 0.00 4.63
3940 4045 8.857694 ATCTAAGACAAAAATTTTAGGACGGA 57.142 30.769 3.34 0.00 0.00 4.69
3941 4046 9.908152 AAATCTAAGACAAAAATTTTAGGACGG 57.092 29.630 3.34 0.00 0.00 4.79
3944 4049 9.705290 GGCAAATCTAAGACAAAAATTTTAGGA 57.295 29.630 3.34 0.00 0.00 2.94
3945 4050 9.710900 AGGCAAATCTAAGACAAAAATTTTAGG 57.289 29.630 3.34 2.55 0.00 2.69
3948 4053 9.710900 CCTAGGCAAATCTAAGACAAAAATTTT 57.289 29.630 0.00 0.00 0.00 1.82
3949 4054 7.819415 GCCTAGGCAAATCTAAGACAAAAATTT 59.181 33.333 29.33 0.00 41.49 1.82
3950 4055 7.323420 GCCTAGGCAAATCTAAGACAAAAATT 58.677 34.615 29.33 0.00 41.49 1.82
3951 4056 6.867550 GCCTAGGCAAATCTAAGACAAAAAT 58.132 36.000 29.33 0.00 41.49 1.82
3952 4057 6.267496 GCCTAGGCAAATCTAAGACAAAAA 57.733 37.500 29.33 0.00 41.49 1.94
3953 4058 5.897377 GCCTAGGCAAATCTAAGACAAAA 57.103 39.130 29.33 0.00 41.49 2.44
3968 4073 0.521735 CCGTTTCAGTTTGCCTAGGC 59.478 55.000 27.71 27.71 42.35 3.93
3969 4074 1.165270 CCCGTTTCAGTTTGCCTAGG 58.835 55.000 3.67 3.67 0.00 3.02
3970 4075 0.521735 GCCCGTTTCAGTTTGCCTAG 59.478 55.000 0.00 0.00 0.00 3.02
3971 4076 1.231958 CGCCCGTTTCAGTTTGCCTA 61.232 55.000 0.00 0.00 0.00 3.93
3972 4077 2.551912 CGCCCGTTTCAGTTTGCCT 61.552 57.895 0.00 0.00 0.00 4.75
3973 4078 2.050442 CGCCCGTTTCAGTTTGCC 60.050 61.111 0.00 0.00 0.00 4.52
3974 4079 2.050442 CCGCCCGTTTCAGTTTGC 60.050 61.111 0.00 0.00 0.00 3.68
3975 4080 1.281656 GTCCGCCCGTTTCAGTTTG 59.718 57.895 0.00 0.00 0.00 2.93
3976 4081 2.248835 CGTCCGCCCGTTTCAGTTT 61.249 57.895 0.00 0.00 0.00 2.66
3977 4082 2.444700 ATCGTCCGCCCGTTTCAGTT 62.445 55.000 0.00 0.00 0.00 3.16
3978 4083 2.939261 ATCGTCCGCCCGTTTCAGT 61.939 57.895 0.00 0.00 0.00 3.41
3979 4084 2.125673 ATCGTCCGCCCGTTTCAG 60.126 61.111 0.00 0.00 0.00 3.02
3980 4085 2.433491 CATCGTCCGCCCGTTTCA 60.433 61.111 0.00 0.00 0.00 2.69
3981 4086 3.192922 CCATCGTCCGCCCGTTTC 61.193 66.667 0.00 0.00 0.00 2.78
3982 4087 4.770874 CCCATCGTCCGCCCGTTT 62.771 66.667 0.00 0.00 0.00 3.60
3986 4091 4.530857 CTGTCCCATCGTCCGCCC 62.531 72.222 0.00 0.00 0.00 6.13
3987 4092 4.530857 CCTGTCCCATCGTCCGCC 62.531 72.222 0.00 0.00 0.00 6.13
3988 4093 3.458163 TCCTGTCCCATCGTCCGC 61.458 66.667 0.00 0.00 0.00 5.54
3989 4094 2.348104 TGTCCTGTCCCATCGTCCG 61.348 63.158 0.00 0.00 0.00 4.79
3990 4095 1.218316 GTGTCCTGTCCCATCGTCC 59.782 63.158 0.00 0.00 0.00 4.79
3991 4096 0.320374 TTGTGTCCTGTCCCATCGTC 59.680 55.000 0.00 0.00 0.00 4.20
3992 4097 0.762418 TTTGTGTCCTGTCCCATCGT 59.238 50.000 0.00 0.00 0.00 3.73
3993 4098 1.001974 TCTTTGTGTCCTGTCCCATCG 59.998 52.381 0.00 0.00 0.00 3.84
3994 4099 2.859165 TCTTTGTGTCCTGTCCCATC 57.141 50.000 0.00 0.00 0.00 3.51
3995 4100 2.711009 TCTTCTTTGTGTCCTGTCCCAT 59.289 45.455 0.00 0.00 0.00 4.00
3996 4101 2.123589 TCTTCTTTGTGTCCTGTCCCA 58.876 47.619 0.00 0.00 0.00 4.37
3997 4102 2.930826 TCTTCTTTGTGTCCTGTCCC 57.069 50.000 0.00 0.00 0.00 4.46
3998 4103 3.077359 CCATCTTCTTTGTGTCCTGTCC 58.923 50.000 0.00 0.00 0.00 4.02
3999 4104 2.485814 GCCATCTTCTTTGTGTCCTGTC 59.514 50.000 0.00 0.00 0.00 3.51
4000 4105 2.107204 AGCCATCTTCTTTGTGTCCTGT 59.893 45.455 0.00 0.00 0.00 4.00
4001 4106 2.486982 CAGCCATCTTCTTTGTGTCCTG 59.513 50.000 0.00 0.00 0.00 3.86
4002 4107 2.787994 CAGCCATCTTCTTTGTGTCCT 58.212 47.619 0.00 0.00 0.00 3.85
4003 4108 1.200948 GCAGCCATCTTCTTTGTGTCC 59.799 52.381 0.00 0.00 0.00 4.02
4004 4109 1.200948 GGCAGCCATCTTCTTTGTGTC 59.799 52.381 6.55 0.00 0.00 3.67
4005 4110 1.251251 GGCAGCCATCTTCTTTGTGT 58.749 50.000 6.55 0.00 0.00 3.72
4006 4111 0.529378 GGGCAGCCATCTTCTTTGTG 59.471 55.000 15.19 0.00 0.00 3.33
4007 4112 0.613012 GGGGCAGCCATCTTCTTTGT 60.613 55.000 15.19 0.00 0.00 2.83
4008 4113 1.325476 GGGGGCAGCCATCTTCTTTG 61.325 60.000 15.19 0.00 0.00 2.77
4009 4114 1.000866 GGGGGCAGCCATCTTCTTT 59.999 57.895 15.19 0.00 0.00 2.52
4010 4115 1.932757 AGGGGGCAGCCATCTTCTT 60.933 57.895 15.19 0.00 0.00 2.52
4011 4116 2.286732 AGGGGGCAGCCATCTTCT 60.287 61.111 15.19 0.00 0.00 2.85
4012 4117 2.123982 CAGGGGGCAGCCATCTTC 60.124 66.667 15.19 0.00 0.00 2.87
4013 4118 4.453892 GCAGGGGGCAGCCATCTT 62.454 66.667 15.19 0.00 43.97 2.40
4023 4128 4.247380 GATCGCCAGAGCAGGGGG 62.247 72.222 7.00 3.56 41.59 5.40
4024 4129 4.247380 GGATCGCCAGAGCAGGGG 62.247 72.222 1.24 1.24 42.56 4.79
4025 4130 4.247380 GGGATCGCCAGAGCAGGG 62.247 72.222 0.00 0.00 39.83 4.45
4026 4131 4.598894 CGGGATCGCCAGAGCAGG 62.599 72.222 3.90 0.00 39.83 4.85
4027 4132 3.781770 GACGGGATCGCCAGAGCAG 62.782 68.421 3.90 0.00 39.83 4.24
4028 4133 3.838271 GACGGGATCGCCAGAGCA 61.838 66.667 3.90 0.00 39.83 4.26
4029 4134 4.933064 CGACGGGATCGCCAGAGC 62.933 72.222 3.90 0.00 45.52 4.09
4077 4182 4.796495 CGAAGGGGGCGGAAAGGG 62.796 72.222 0.00 0.00 0.00 3.95
4106 4211 3.186047 CGACACATCCGCCGGAAC 61.186 66.667 11.19 0.00 34.34 3.62
4113 4218 4.873129 CGAGGGGCGACACATCCG 62.873 72.222 0.00 0.00 44.57 4.18
4136 4241 4.587189 GATCGAAGGGGCGTCCGG 62.587 72.222 0.00 0.00 41.52 5.14
4137 4242 4.925576 CGATCGAAGGGGCGTCCG 62.926 72.222 10.26 0.00 41.52 4.79
4183 4288 2.125106 GGGTCATCGGCACAGTCC 60.125 66.667 0.00 0.00 0.00 3.85
4184 4289 2.125106 GGGGTCATCGGCACAGTC 60.125 66.667 0.00 0.00 0.00 3.51
4185 4290 3.717294 GGGGGTCATCGGCACAGT 61.717 66.667 0.00 0.00 0.00 3.55
4199 4304 3.744155 GGGGAGCAGGAAAGGGGG 61.744 72.222 0.00 0.00 0.00 5.40
4200 4305 4.115199 CGGGGAGCAGGAAAGGGG 62.115 72.222 0.00 0.00 0.00 4.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.